SMTL ID : 7kbg.2 (2 other biounits)

Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.177, H.179, D.265, G.302 Ligands: WBA.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.177, A:H.179, A:D.265

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.177, A:H.179, A:S.198, A:F.199 CA.3: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.4, H2O.10

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: E.87, Y.88, K.90, Q.91 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.90, A:Q.91 Water bridges: A:S.89, A:R.94 Salt bridges: A:K.90 SO4.5: 2 residues within 4Å: Chain A: R.271, R.307 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.307 Salt bridges: A:R.271, A:R.307 SO4.8: 3 residues within 4Å: Chain A: K.248, F.368, R.372 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.248 Salt bridges: A:K.248, A:R.372

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 1 residues within 4Å: Chain A: N.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.350 PEG.7: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.105 Water bridges: A:D.19, A:N.22, A:D.105, A:D.105

1 x WBA: N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl)amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide(Non-covalent)

WBA.9: 22 residues within 4Å: Chain A: G.28, H.29, P.30, M.31, E.99, D.100, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, G.301, G.302, Y.304 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.30, A:E.99, A:F.151, A:F.151, A:F.206, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:D.100, A:G.150, A:G.302, A:Y.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group. Acs Med.Chem.Lett. (2020)

Release Date

2020-12-30

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 2

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